- Jan 2021
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academic.oup.com academic.oup.com
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Jonathan Eisen on the issues surrounding this work is published alongside this article
And see also the coverage in the WSJ https://www.wsj.com/articles/SB10000872396390444840104577551433143153716
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academic.oup.com academic.oup.com
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northern Europe
New migrations to the UK are being tracked by citizen science projects to see if this is related to climate change http://srs.britishspiders.org.uk/portal/p/Wasp+Spider
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- Dec 2020
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Abstract
Can watch a video abstract with the author here https://youtu.be/8T-lwGEGlGs
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academic.oup.com academic.oup.com
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The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy community provide a means for users to learn, publish, and teach single-cell RNA-sequencing analysis.
See the write-up by the Earlham Institute for more on how this training is going on
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- Oct 2020
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academic.oup.com academic.oup.com
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uploaded to IDseq from Phnom Penh, Cambodia
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Background
For more background see GigaBlog http://gigasciencejournal.com/blog/idseq-infectious-disease-detectives/
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- Aug 2020
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academic.oup.com academic.oup.com
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Consortia Advancing Standards in Research Administration Information (CASRAI) contributorship taxonomy
Which has now become NISO CRediT (Contributor Roles Taxonomy), see http://credit.niso.org/
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- Jul 2020
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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All supporting data and materials are available in the GigaScience database, GigaDB [48].
Sequencing data is also in NCBI via BioProject: PRJNA576514 and proteomics data is in PRIDE: PXD018943
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academic.oup.com academic.oup.com
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functional magnetic resonance imaging (fMRI)
This paper (and data type) gets a mention in GigaBlog http://gigasciencejournal.com/blog/guest-blog-challenges-and-opportunities-with-sharing-neuroimaging-data/
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fMRI dataset
Part of our fMRI series: https://academic.oup.com/gigascience/pages/fmri_advances_and_challenges
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10.5524/100051
Data in GigaDB here: http://dx.doi.org/10.5524/100051
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academic.oup.com academic.oup.com
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BGISEQ-500
Now known as DNBSEQ-G50
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- Jun 2020
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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The annual Parasite Awards
See Parasite Award website here: https://researchparasite.com/
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SRA and Gene Expression Omnibus (GEO)
See the NCBI short read archive (SRA) and Gene Expression Omnibus (GEO) databases here:
https://www.ncbi.nlm.nih.gov/sra/ https://www.ncbi.nlm.nih.gov/geo/
Other centralized data repositories are available.
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In 2018, eLife published a demonstration
Read more about eLife's reproducible document stack here https://elifesciences.org/labs/b521cf4d/reproducible-document-stack-towards-a-scalable-solution-for-reproducible-articles
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VMs
We wrote about our first experiences publishing virtual machines back in 2014 http://gigasciencejournal.com/blog/publishing-our-first-virtual-box-of-delights-to-aid-the-fight-against-heart-disease/
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Hypothes.is
GigaScience has hypothes.is integration, and you can read more about how we are using it to add value to papers in this GigaBlog posting http://gigasciencejournal.com/blog/hypothes-is-integration/
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academic.oup.com academic.oup.com
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teaching hands-on genome assembly courses
Another example is the Bauhinia Genome project that has used the crowdfunded genomics data to educated the public and teach MSc students at the Chinese University of Hong Kong genome assembly http://bauhiniagenome.hk/2018/03/crowdfunded-genomes-and-the-plant-genome-big-bang/
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even small research groups
There have even been community funded genome projects such as the "peoples parrot" and Azolla genome project, with strong education components such as this one (although using short reads to make an initial draft genome) http://gigasciencejournal.com/blog/community-genomes-from-the-peoples-parrot-to-crowdfernding/
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academic.oup.com academic.oup.com
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pig gut
Pig gut dataset in GigaDB http://dx.doi.org/10.5524/100187
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- May 2020
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academic.oup.com academic.oup.com
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availability of gene reference catalogs from gut microbiomes
Like this data many hosted in our GigaDB repository, and this has been covered in more detail in GigaBlog http://gigasciencejournal.com/blog/monkey-microbiome/
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academic.oup.com academic.oup.com
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first two penguin genomes
All the remaining penguin species have now also been sequenced in a follow-up study, see https://doi.org/10.1093/gigascience/giz117
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academic.oup.com academic.oup.com
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http://www.gigasciencejournal.com/content/3/1/27
This URL doesn't work any more but the DOI redirects it to the new location https://doi.org/10.1186/2047-217X-3-27
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rvhost-alpha.rivervalleytechnologies.com rvhost-alpha.rivervalleytechnologies.com
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Members of the Free State Society for the Blind putting the 3D models through a trial run at a recent visit to the Museum
Coverage of this here https://nationalmuseumpublications.co.za/making-the-untouchable-touchable/
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National Museum in Bloemfontein
See museum website here https://nasmus.co.za/
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will be released
Eventually published in GigaDB http://dx.doi.org/10.5524/100627
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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accumulate potent phytotoxins
Inspiring the film "The Birds", which you can read more in the Sanger Institute blog https://sangerinstitute.blog/2020/05/04/prising-open-the-scallop-genome/
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Katherine James Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK Search for other works by this author on: Oxford Academic Google Scholar Katherine James, Emma Betteridge Wellcome Sanger Institute, Cambridge CB10 1SA, UK Search for other works by this author on: Oxford Academic Google Scholar
This Q&A features some discussion of her contribution to this project
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- Apr 2020
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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Wellcome Sanger 25 Genomes Project
This project's goal is to sequence 25 novel genomes representing UK biodiversity, as part of the Wellcome Sanger Institute's wider 25th Anniversary celebrations. See https://www.sanger.ac.uk/science/collaboration/25-genomes-25-years
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academic.oup.com academic.oup.com
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Rhopilema esculentum (Kishinouye, 1891)
Also known as the flame jellyfish https://en.wikipedia.org/wiki/Rhopilema_esculentum
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several genome assemblies have been reported
We've published and written more on some of these genomes here: http://gigasciencejournal.com/blog/jellyfish-genomes/
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interspecies F1 hybrid of yak (Bos grunniens, NCBI:txid30521) and cattle (Bos taurus, NCBI:txid9913)
In Tibet this type of yak-cow hybrid is know as a "dzo" (མཛོ)་ https://en.wikipedia.org/wiki/Dzo
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Timothy P L Smith US Meat Animal Research Center, US Department of Agriculture, State Spur 18D, Clay Center, NE 68933, USA Correspondence address. Timothy P. L. Smith, US Meat Animal Research Center, US Department of Agriculture, Clay Center, NE 68933, USA. E-mail: tim.smith2@usda.gov http://orcid.org/0000-0003-1611-6828 Search for other works by this author on: Oxford Academic Google Scholar Timothy P L Smith
See the Q&A with Benjamin Rosen and Timothy Smith in GigaBlog for more insight http://gigasciencejournal.com/blog/dna-day-2020-cattle-reference-genome/
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academic.oup.com academic.oup.com
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Benjamin D Rosen
See the Q&A with Benjamin Rosen & Timothy Smith in GigaBlog for more insight into this work http://gigasciencejournal.com/blog/dna-day-2020-cattle-reference-genome/
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L1 Dominette
NPR has covered this famous cow https://www.npr.org/templates/story/story.php?storyId=103382511
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academic.oup.com academic.oup.com
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progression of respiratory diseases
Including COVID-19, as it is estimated 50% of patients with COVID-19 who have died had secondary bacterial infections. Watch the COSMIC project looking at metagenomics of respiratory samples to identify the bacteria, fungi, and viral co-infections present in patients with COVID-19 https://www.covid-coinfections.org/t/cosmic-co-infections-and-secondary-microbial-infections-in-covid-19/17
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Supplemental File 1: Extended Chinese language (中文版) version on the editorial.
See also a Chinese language adaptation of this statement in Bull. Ntnl. Nat. Sci Foundation China. http://www.cnki.net/kcms/doi/10.16262/j.cnki.1000-8217.2018.06.001.html
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A version of the editorial translated into Chinese is included as a Supplementary File
See also a Chinese language adaptation of this statement in Bull. Ntnl. Nat. Sci Foundation China. http://www.cnki.net/kcms/doi/10.16262/j.cnki.1000-8217.2018.06.001.html
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Here, we help clarify this and also provide a clear statement of our expectations around how authors are assigned to manuscripts submitted to GigaScience.
A more detailed version of this clarification and background is available via our blog: http://gigasciencejournal.com/blog/appropriate-authorship/
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Laurie Goodman
‡ Senior author
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Abstract
This was a winner of the 2018 GigaScience prize and presented at the ICG13 conference in Shenzhen. See video here https://youtu.be/7W6EDZhnvb4
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academic.ouprc.silverchair.com academic.ouprc.silverchair.com
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Background
A Keynote on Open Humans was presented by author Madeline Ball at BOSC (Bioinformatics Open Source Conference) and is viewable here https://youtu.be/CegpG10VPvM
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academic.oup.com academic.oup.com
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Abstract
You can watch a video presentation of this work recorded at the Galaxy Community Conference from author Nicola Soranzo here https://vimeo.com/296964100
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academic.oup.com academic.oup.com
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"Nala" the female German Shepherd Dog. Nala, or formally “Jonkahra Nala” (Australian Registration #2100398550)
More on Nala in the Vet Candy blog https://www.myvetcandy.com/clinicalupdblog/2020/4/2/first-complete-german-shepherd-dna-offers-new-tool-to-fight-disease
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Findings
Coverage in GenomeWeb https://www.genomeweb.com/scan/german-shepherds-own-sequence#.XoeoXG4o-qA
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- Mar 2020
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academic.oup.com academic.oup.com
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which is the basis of our planned second release (PLINK 2.0).
See the homepage for updates taking it towards PLINO 2.0 alpha https://www.cog-genomics.org/plink/2.0/
We also have phased and annotated data for use in plink2.0 worked examples in GigaDB http://dx.doi.org/10.5524/100516
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3.Li Z, Barker MS. Inferring putative ancient whole genome duplications in the 1000 Plants (1KP) initiative: Access to gene family phylogenies and age distributions. bioRxiv. 2019:735076. https://www.biorxiv.org/content/10.1101/735076v1.
A peer reviewed and updated version of this has now been published in GigaScience https://doi.org/10.1093/gigascience/giaa004
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chlorophyte green algae
Some of the authors have recorded a podcast discussing the implications for algae research from this data https://podcasts.apple.com/us/podcast/gane-ka-shu-wong-michael-melkonian-on-if-algae-can/id1420197433?i=1000458893924
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academic.ouprc.silverchair.com academic.ouprc.silverchair.com
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Article history
GigaScience carry out Open Peer review and you can read the peer reviews via these DOIs:
Joon-Ho Yu: http://dx.doi.org/10.5524/REVIEW.101788 Birgit Wouters: http://dx.doi.org/10.5524/REVIEW.101787
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Abstract
This has been recommended and reviewed by F1000 https://f1000.com/prime/731984614
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Abstract
This has been recommended and reviewed by F1000 https://f1000.com/prime/734961664
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Abstract
This has been recommended and reviewed by F1000 here https://f1000.com/prime/735958664
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academic.oup.com academic.oup.com
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Abstract
This has been highlighted and reviewed by F1000 https://f1000.com/prime/718180400
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europepmc.org europepmc.org
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hypothes.is (use the hashtag/tag #chromosomenomenclature)
Please add comments directly on the key parts of the commentary you would like to raise any issues with.
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academic.oup.com academic.oup.com
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forensic investigations
Some examples of forensic entomology highlighted here https://www.wired.com/2013/10/when-crime-scene-evidence-crawls-away/
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academic.oup.com academic.oup.com
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Access to OUP resources on COVID-19, other coronaviruses, and related topics
30 leading publishers have all made their coronavirus related content open access in this manner https://wellcome.ac.uk/press-release/publishers-make-coronavirus-covid-19-content-freely-available-and-reusable
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gigasciencejournal.com gigasciencejournal.com
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Guest Blog: Data in the time of Coronavirus
This follows on from previous infectious disease modelling guest blogs from Dr Mike Dean on Ebola http://gigasciencejournal.com/blog/guest-blog-the-2014-ebola-epidemic-approaches-and-resources-to-slow-the-spread-of-infection/ and Zika http://gigasciencejournal.com/blog/guest-blog-mind-zika-data-gap/
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academic.oup.com academic.oup.com
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Table S3. Representative applications of genome editing. A summary of the representative applications in different organisms.
Using hypothes.is this information can also be updated via annotations here. e.g. adding mention of Twist biosciences, whose Oligo pools are utilized in many CRISPR applications including generation of CRISPR guide RNA (sgRNA) libraries. See https://www.twistbioscience.com/products/oligopools
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Table S1. Online tools for TALEN and CRISPR/Cas9. Collected online tools for TALEN and CRISPR/Cas9 are presented in this table. Updates can be accessed in GitHub [107]. Table S2. Commercial service for TALEN and CRISPR/Cas9. Collected commercial service for TALEN and CRISPR/Cas9 are presented in this table. Updates could can accessed in GitHub [107]. Table S3. Representative applications of genome editing. A summary of the representative applications in different organisms.
Given that new methods, kits, and services continue to be rapidly developed and updated, an editable version we set up on Github wiki, and readers encourage to update it. See https://github.com/gigascience/paper-chen2014/wiki
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academic.oup.com academic.oup.com
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Here, we present the first chromosome-level genome assembly and gene annotation of A. sinensis.
See some media coverage of this work here https://news.cgtn.com/news/2020-03-24/Scientists-release-genome-of-agarwood-tree-Aquilaria-sinensis-P7q0PlxXmo/index.html
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excessively exploited
Despite being the reason Hong Kong was known as the "fragrant harbour" these tree's are heavily poached and nearly extinct in the wild in Hong Kong http://www.bbc.com/travel/story/20170306-the-scent-thats-pricier-than-gold
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academic.oup.com academic.oup.com
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This must be achieved by sequencing and archiving huge numbers of microbial genomes, both from clinical cases and known environmental reservoirs, on a continual basis.
Even without reference genomes, mining metagenomes for coronavirus sequences has become particularly topical in 2020. See the Pangolin 2019-nCoV-like coronavirus example https://doi.org/10.1101/2020.02.08.939660
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swine flu
Jennifer Gardy discusses the groundbreaking H1N1 crowdsourcing efforts in her TEDx talk here (with lots of lessons for the coronavirus outbreak a decade later) https://www.youtube.com/watch?v=LmAugMSJ1-Y
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Escherichia coli O104: H4
See more in GigaBlog about the novel "tweenome" method of datasharing for this project http://gigasciencejournal.com/blog/notes-from-an-e-coli-tweenome-lessons-learned-from-our-first-data-doi/
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academic.oup.com academic.oup.com
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MERS coronavirus
Mining metagenomes for coronavirus sequences has become particularly topical in 2020 (see the Pangolin 2019-nCoV-like coronavirus example https://doi.org/10.1101/2020.02.08.939660)
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RNA viruses
As this works with RNA viruses it has been made part of the "Free access to OUP resources on coronavirus and related topics" collection on the Oxford University Press website https://academic.oup.com/journals/pages/coronavirus
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academic.oup.com academic.oup.com
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direct RNA sequencing. Despite the scientific relevance of VACV, no LRS data have been generated for the viral transcriptome to date.
This approach of using Oxford Nanopore direct-RNA sequencing for viruses has now been carried out on the SARSCov2/COVID19 causing coronavirus. See https://doi.org/10.1101/2020.03.05.976167
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academic.oup.com academic.oup.com
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galaxy-based viral genome assembly pipeline
This galaxy + viral genome assembly approach has been updated in 2020 to analyze and store COVID19/SARSCov2 data https://covid19.galaxyproject.org/
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- Feb 2020
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academic.oup.com academic.oup.com
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Taylor J Noble
Taylor Noble video abstract: https://youtu.be/NQjmxE4Frxo
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academic.oup.com academic.oup.com
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Ocean Sampling Day
One of the authors has presented a talk on the Citizen Science offshoot of this project here https://youtu.be/t6WpLbd0Nf8
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academic.oup.com academic.oup.com
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Critical Assessment of Metagenome Interpretation (CAMI) initiative
See the CAMI website https://data.cami-challenge.org/
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academic.oup.com academic.oup.com
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Since 1996
The Fort Lauderdale agreement followed these up in 2003, but there has been a long gap since then https://www.genome.gov/10506537/reaffirmation-and-extension-of-nhgri-rapid-data-release-policies
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- Oct 2019
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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detections in surrounding states
And it has just been reported in Connecticut https://www.nbcconnecticut.com/news/local/Destructive-Spotted-Lanternfly-Spotted-in-Connecticut-563208361.html
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Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell.
See the press release here discussing the novelty of this data https://www.eurekalert.org/pub_releases/2019-10/udoa-fgo101619.php
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Eudyptes moseleyi Northern rockhopper Wild Amsterdam Island NRP 118–1 May 2016
Data in GigaDB here: http://dx.doi.org/10.5524/102171
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europepmc.org europepmc.org
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Saccharomyces cerevisiae
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African eggplant
Also know as the scarlet eggplant or bitter tomato.
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“orphan crop”
The African eggplant is a good example of the work of the Africa Orphan Crop consortium and many of the authors are consortium members. You can read more on the first genomes released in GigaBlog here: http://gigasciencejournal.com/blog/democratising-data-aocc/
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